Posts by Andrew Cosgrove

Twins to win

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To mark the passing of the sun into Gemini, this month Genome Biology has published a special issue on twin studies. Not really: we just had a lot of twin studies and they all fortuitously ended up being published in May. But they’re good studies, so we thought it was worth highlighting them here.

Human genomics is mostly correlative: a genetic variant is seen to be associated with a given phenotype. In some cases, the association might be strong enough to infer a cause, but as everyone knows, correlation is no proof of causation. Unfortunately, the sort of confirmatory functional work that might be possible in laboratory animals is usually frowned upon by pesky ethics committees if you propose …

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Beetlemania

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Credit: Ward Strong, B.C. Ministry of Forests, Lands, and Natural Resource Operations.

JBS Haldane famously remarked that the Creator appears to be inordinately fond of beetles – with over 400,000 species described, they make up over a quarter of all known animal species. This enthusiasm has not been shared by genomicists. Only a single beetle genome has been completed, that of the red flour beetle, Tribolium castaneum. Now, a new publication in Genome Biology DOUBLES our knowledge of beetle genomes, by describing the sequencing and assembly of the genome of the mountain pine beetle, Dendroctonus ponderosae.

D. ponderosae is a species of bark beetle native to North America. The beetles lay eggs under the bark of various species of pine trees and then release pheromones to attract more beetles. When the eggs …

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Latest issue of Genome Biology

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Following on from Naomi’s blog on the highlights of 2012 in Genome Biology, I’m going to expand on her mention of our cancer articles. We published four cancer-related articles in December: two Research, and two Methods.

Jinghui Zhang and colleagues from the St Jude Hospital in Memphis, together with collaborators from Washington University, St Louis and the Memorial Sloan-Kettering Cancer Center in New York, have assessed the telomere content of a large panel of pediatric cancers. Telomeres are the specialized structures at the ends of chromosomes that, in normal cells, shorten with every cell division. Once they have shortened to reach a critical length threshold, the cells are unable to divide further. Since cancer is a disease …

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Detecting low frequency mutations

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In most genome sequencing applications, at a given locus there are at most two variants, present in equal proportions (ie the two alleles in a diploid individual). In situations like these, the high error rates of next generation sequencing technology are not a large problem, as any errors are likely to be present at much lower frequency than reads from the true variants, so are easy to filter out. There are some situations, however, where variants are present at low frequency in the sample. Examples would include sequencing a tumor, which is a collection of cells all of whose genomes may have diverged from the founder cell; sequencing mitochondrial genomes, as each cell contains many mitochondria, not all of which …

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Nurse! The screens!

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37 years ago, Paul Nurse performed a screen in the fission yeast Schizosaccharomyces pombe for mutants which divided at an abnormally small size. He identified a gene, wee1, which was the first gene found to control the cell cycle and cell division. As a result of this work, Nurse won the Nobel Prize for Physiology or Medicine in 2001, together with Lee Hartwell and Genome Biology editorial board member Tim Hunt. This work has been built on over time, such that we now have a good picture of the events that coordinate cell division with cell growth, but there are still gaps in our knowledge. For instance, it is clear that there must be pathways other than …

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GigaScience – a repository for large datasets

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The recent explosion of genomics technology has revolutionized biology, but it is only really of use if people are able to analyze and use the resulting sequences. Storage of such vast quantities of data is problematic, as the ongoing uncertainty over the future of NCBI’s arm of the Sequence Read Archive shows (SRA). The BGI, in conjunction with BioMed Central, recently launched GigaScience, a journal aimed specifically at projects generating a lot of data, which can accommodate such large datasets alongside the articles describing them. GigaScience also anticipates becoming a repository for stand-alone datasets such as those resulting from genome sequencing projects. One such dataset has just been released, and it contains the assembled and annotated sequences …

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Genome Biology – highlights of the October issue

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The October issue of Genome Biology is now available and, excitingly, it contains reports of three novel genome sequences.

Much attention has already surrounded our article from van Bakel et al. reporting the genome of Cannabis sativa. As well as sequencing and assembling the genome, the group also sequenced the transcriptomes of the Purple Kush marijuana strain and the Finola hemp strain to shed light on why marijuana is psychoactive and hemp is not. So as not to spoil the surprise, I won’t reveal the answer here – read the article, or our editorial by Naomi Attar, to find out.

The liver fluke Clonorchis sinensis is endemic in South East Asia and is the third most prevalent worm …

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Genome Biology – lots of exciting software this month

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The August issue of Genome Biology is now available on our website, and it’s a bumper issue this month. As well as several high-quality research articles (such as the wallaby genome sequence, the transcriptome of regenerating heads in planarians and a comprehensive screen for substrates of the Chk1 checkpoint kinase), we have a number of exciting computational methods for analyzing high throughput genomics data.

Kim and Salzberg present TopHat-Fusion, a modified version of the popular TopHat package for analyzing RNA-seq datasets, that can identify transcripts from fusion genes. As fusion genes are often important in carcinogenesis (such as the canonical BCR-Abl fusion from the Philadelphia chromosome in some leukemias), this has important medical applications.

Uwe Ohler …

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Companion articles explore the kangaroo genome

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Accompanying the publication of the tammar wallaby genome sequence in  Genome Biology, BioMed Central also has a pouchful of companion articles in a cross-journal article series.

The focus of several of these studies is on the insights that the genome sequence offers into marsupial immune systems. Emily Wong and colleagues present a database of immune genes identified from several marsupial and monotreme species. This gives researchers a new tool for exploring immune function in these groups and more broadly in understanding the evolution of the mammalian  immune system. In another study, Wong et al. also compare the genes expressed in the twin thymus glands of wallabies to understand the immune function of each organ, finding that both are …

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Genome Biology editorial on the closure of NCBI’s SRA

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The US government-funded National Center for Biotechnology Information (NCBI) has recently announced that it will be withdrawing funding for its Sequence Read Archive (SRA), its repository for short read sequencing data. At BioMed Central we hold that the free availability of data is a key requirement for scientific work, and so we have been routinely asking authors submit their data to the SRA. The closure of the SRA will thus affect authors and  journals’ policies on data availability.

To try to clear up some of the uncertainty surrounding the NCBI’s announcement, Genome Biology canvassed the opinions of five scientists with interest in the closure of the database, either through being involved in maintenance of the database itself, or as …

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